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Labs at CAGT

  • Biomolecular Systems (BSL) Laboratory is directed by Dr. DeLisi. BSL develops and applies computational/mathematical methods, and high throughput experimental methods, to analyze changes in gene and protein expression profiles of cells in response to various endogenous and exogenous signals. In collaboration with the Fraunhofer Center for Manufacturing Innovation, and the Departments of Chemistry and Physics, we are developing and applying new DNA and peptide microarray technologies for fingerprinting the complete molecular state of a cell. Examples include the response to ligands (drugs, toxins, hormones etc), and changes that occur as normal cells mature, differentiate, progress toward disease. The long range goal is to relate expression patterns to pathways, pathways to networks and networks to function.
  • Protein Engineering is also known as Zhiping's Lab. It has two components: the computational component still needs a catchy name, while the experimental component is called the Protein Engineering Laboratory. Led by Dr. Zhiping Weng, we are a bunch of young people eager to establish careers in Bioinformatics and Biomolecular Engineering. Trying very hard not to be interested in everything, we focus our research on molecular interactions, such as (1) interaction between regulatory proteins and their DNA/RNA target sites (2) protein-protein interaction (3) protein-peptide interaction (4) interaction between protein structure building blocks. ZLAB has two major projects:
  • Computational Genomics lab (directed by Professor Simon Kasif) has a goal to collaborate with biologists in the design of novel biological experiments that can be coupled with innovative computational analysis and modeling in order to improve our understanding of gene function. Biological organisms are qualitatively modelled as probabilistic networks of genes and proteins generating cascades of induction and regulation of other genes and proteins. In addition to identifying new genes and assigning them broad biological functions, the lab is involved in building qualitative or probabilistic computational frameworks that can integrate experimental data and provide us with the ability to predict with high accuracy the behavior of cells in normal or perturbed conditions. Such analytical capabilities will have a strong impact on drug design and screening, diagnostics as well as basic biological and medical sciences.
  • Structural Bioinformatics lab, headed by Sandor Vajda, focuses on the recognition of proteins and small molecules by protein receptors. Studying protein-protein interactions is crucial for a better understanding of processes such as metabolic control, signal transduction, and gene regulation, whereas the ability to dock small ligands to proteins is the key to rational drug and vaccine design strategies. Both problems become much more difficult if no x-ray structure of the protein is available. Accordingly, our main research areas are (1) the development of efficient protein docking algorithms, (2) docking of small ligands to proteins, primarily for the characterization of binding sites, and (3) homology modeling of proteins.
  • Laboratory for Biocomputing and Informatics (LBI) is a research lab led by Dr. Gary Benson. This laboratory's research focuses on development of algorithms and software tools for the detection and analysis of novel patterns and repeats in DNA and RNA sequences. Among our interests are new methods to search for tandem and inverted repeats, alignment and clustering algorithms, seed optimizations and many others.
  • Daniel Segre' lab is interested in the evolutionary dynamics of biological networks, in particular in the interplay between response to genetic and environmental perturbations, genomic-level functional organization, and optimal adaptation. Goals include developing constraint-based models to study the regulatory and evolutionary dynamics of metabolic networks across different organisms, cell types, and interacting cell populations.
  • Yu Xia lab is in the Bioinformatics Program and the Department of Chemistry at Boston University. Research in the lab is focused on computational systems biology. We apply computational techniques to study the structure, function, and evolution of complex bio-molecular systems, such as proteins and protein networks. Specific projects include: modeling and simulation of proteins and protein networks; comparative and evolutionary analysis of proteins and protein networks; protein sequence-structure-function relationships; prediction of protein structure and function.
Protein Engineering